Variant rs3803231 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001846.4(COL4A2):c.2039-45T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 1,612,008 control chromosomes in the GnomAD database, including 8,902 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.10 ( 878 hom., cov: 32)

Exomes 𝑓: 0.10 ( 8024 hom. )

Consequence

COL4A2
NM_001846.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.64

Variant links:

Genes affected

COL4A2 (HGNC:2203): (collagen type IV alpha 2 chain) This gene encodes one of the six subunits of type IV collagen, the major structural component of basement membranes. The C-terminal portion of the protein, known as canstatin, is an inhibitor of angiogenesis and tumor growth. Like the other members of the type IV collagen gene family, this gene is organized in a head-to-head conformation with another type IV collagen gene so that each gene pair shares a common promoter. [provided by RefSeq, Jul 2008]

COL4A2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 13-110466995-T-C is Benign according to our data. Variant chr13-110466995-T-C is described in ClinVar as [Benign]. Clinvar id is 1264114.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL4A2	NM_001846.4 linkuse as main transcript	c.2039-45T>C		intron_variant		ENST00000360467.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL4A2	ENST00000360467.7 linkuse as main transcript	c.2039-45T>C		intron_variant		5	NM_001846.4	P1

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

15851

AN:

151958

Hom.:

876

Cov.:

show subpopulations

Gnomad AFR

AF:

0.102

Gnomad AMI

AF:

0.0954

Gnomad AMR

AF:

0.110

Gnomad ASJ

AF:

0.138

Gnomad EAS

AF:

0.109

Gnomad SAS

AF:

0.100

Gnomad FIN

AF:

0.0774

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.106

Gnomad OTH

AF:

0.123

GnomAD3 exomes

AF:

0.108

AC:

26706

AN:

248124

Hom.:

1544

AF XY:

0.108

AC XY:

14503

AN XY:

134686

show subpopulations

Gnomad AFR exome

AF:

0.102

Gnomad AMR exome

AF:

0.119

Gnomad ASJ exome

AF:

0.145

Gnomad EAS exome

AF:

0.127

Gnomad SAS exome

AF:

0.108

Gnomad FIN exome

AF:

0.0768

Gnomad NFE exome

AF:

0.104

Gnomad OTH exome

AF:

0.113

GnomAD4 exome

AF:

0.103

AC:

150543

AN:

1459932

Hom.:

8024

Cov.:

AF XY:

0.103

AC XY:

75049

AN XY:

726254

show subpopulations

Gnomad4 AFR exome

AF:

0.105

Gnomad4 AMR exome

AF:

0.118

Gnomad4 ASJ exome

AF:

0.143

Gnomad4 EAS exome

AF:

0.0838

Gnomad4 SAS exome

AF:

0.108

Gnomad4 FIN exome

AF:

0.0730

Gnomad4 NFE exome

AF:

0.103

Gnomad4 OTH exome

AF:

0.110

GnomAD4 genome

AF:

0.104

AC:

15864

AN:

152076

Hom.:

878

Cov.:

AF XY:

0.103

AC XY:

7676

AN XY:

74350

show subpopulations

Gnomad4 AFR

AF:

0.102

Gnomad4 AMR

AF:

0.109

Gnomad4 ASJ

AF:

0.138

Gnomad4 EAS

AF:

0.109

Gnomad4 SAS

AF:

0.100

Gnomad4 FIN

AF:

0.0774

Gnomad4 NFE

AF:

0.106

Gnomad4 OTH

AF:

0.121

Alfa

AF:

0.111

Hom.:

1358

Bravo

AF:

0.110

Asia WGS

AF:

0.100

AC:

347

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.032

DANN

Benign

0.26

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over